TY - JOUR T1 - LinkedSV: Detection of mosaic structural variants from linked-read exome and genome sequencing data JF - bioRxiv DO - 10.1101/409789 SP - 409789 AU - Li Fang AU - Charlly Kao AU - Michael V Gonzalez AU - Fernanda A Mafra AU - Renata Pellegrino da Silva AU - Mingyao Li AU - Hakon Hakonarson AU - Kai Wang Y1 - 2018/01/01 UR - http://biorxiv.org/content/early/2018/10/10/409789.abstract N2 - Reliable detection of structural variants (SVs) from short-read sequencing remains challenging, mainly due to the presence of repetitive DNA elements that are longer than typical short reads (~100-150bp). Linked-read sequencing provides long-range information from short-read sequencing data by linking reads originating from the same HMW DNA molecule, and thus has the potential to improve the sensitivity of SV detection and accuracy of breakpoint identification for certain classes of SVs. We present LinkedSV (https://github.com/WGLab/LinkedSV), a novel SV detection algorithm which combines two types of evidence. Simulation and real data analysis demonstrated that LinkedSV outperforms several existing tools including Longranger, GROC-SVs and NAIBR. LinkedSV works particularly well on exome sequencing data and on SVs with low variant allele frequencies due to somatic mosaicism. Our results support the use of linked-read sequencing to detect hidden SVs missed by conventional short-read sequencing approaches and helps resolve negative cases from clinical genome or exome sequencing. ER -